Variant report

Variant	rs9321104
Chromosome Location	chr6:128330249-128330250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr6:128327652-128330742	HepG2	liver:	n/a	chr6:128328818-128328830

Variant related genes	Relation type
PTPRK	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11759373	1.00[CHD][hapmap]
rs12194062	1.00[CHD][hapmap]
rs156062	1.00[CHD][hapmap]
rs2064388	0.97[EUR][1000 genomes]
rs270002	1.00[CHD][hapmap]
rs270003	1.00[CHD][hapmap]
rs4573107	1.00[CHD][hapmap]
rs4596504	1.00[CHD][hapmap]
rs6569519	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6921729	1.00[CHD][hapmap]
rs699416	1.00[CHD][hapmap]
rs699417	1.00[CHD][hapmap]
rs7749132	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7749500	1.00[EUR][1000 genomes]
rs7772658	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs9375542	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs9388608	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9398863	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9402010	0.95[EUR][1000 genomes]
rs9491896	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9491897	1.00[CEU][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604642	chr6:128278798-128351143	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9321104	THEMIS	cis	cerebellum	SCAN
rs9321104	ENPP3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128289000-128431000	Weak transcription	Psoas Muscle	Psoas
2	chr6:128293600-128374400	Weak transcription	Pancreas	Pancrea
3	chr6:128294400-128330600	Weak transcription	NHDF-Ad	bronchial
4	chr6:128297400-128334000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:128298000-128352600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:128298200-128334600	Weak transcription	Fetal Heart	heart
7	chr6:128302600-128331400	Weak transcription	Gastric	stomach
8	chr6:128302800-128343800	Weak transcription	Ovary	ovary
9	chr6:128305200-128353000	Weak transcription	Left Ventricle	heart
10	chr6:128306000-128334000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:128306000-128343200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:128307200-128340800	Weak transcription	HSMMtube	muscle
13	chr6:128307800-128370800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:128311600-128387200	Weak transcription	NH-A	brain
15	chr6:128311800-128378400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:128314000-128367400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:128320400-128340600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:128320600-128330600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:128320800-128334200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:128320800-128350200	Weak transcription	Fetal Thymus	thymus
21	chr6:128320800-128357800	Weak transcription	Fetal Intestine Small	intestine
22	chr6:128320800-128388200	Weak transcription	NHEK	skin
23	chr6:128322400-128332800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:128326400-128338200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:128326400-128342800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:128326400-128351000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:128326600-128330800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:128326600-128331200	Weak transcription	Osteobl	bone
29	chr6:128326600-128343400	Weak transcription	Fetal Intestine Large	intestine
30	chr6:128326600-128356600	Weak transcription	HSMM	muscle
31	chr6:128326600-128388200	Weak transcription	HMEC	breast
32	chr6:128327000-128340800	Weak transcription	Primary B cells from cord blood	blood
33	chr6:128329200-128353000	Weak transcription	HepG2	liver
34	chr6:128330000-128330400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:128330200-128353000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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